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Releases: nglviewer/ngl

v0.9.3

15 Oct 00:29
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Changed

  • increased light distance from camera, to fix unlit rendering
  • remove double quotes from atomnames in chemComp cif parser

v0.9.2

07 Oct 00:28
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Changed

  • fix, moved polyfills back inside the bundle

v0.9.1

06 Oct 21:23
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Changed

  • removed (wrongly added) ngl2.js from dist folder
  • fixed chemComp cif parser not passing chainid

v0.9.0

05 Oct 17:35
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Added

  • lazy representation parameter that only builds & updates the representation when visible
  • chainname based color scheme
  • BondHash class to quickly get atoms connected to an atom
  • SpatialHash class to quickly get neighboring atoms/points
  • XmlParser parameter to use the browser's DOMParser
  • attachment (top, middle, bottom; left, center, right) for LabelRepresentation/TextBuffer
  • border color and width for LabelRepresentation/TextBuffer
  • colored background rectangle for LabelRepresentation/TextBuffer
  • "offset" style rendering of double/triple bonds (@fredludlow)
  • PubchemDatasource to load cid as sdf, pubchem://16490
  • basic entity support (type, description, chain mapping; mmcif, mmtf)
  • entitytype, moleculetype, chainid, polymer color schemes
  • ShaderRegistry, DecompressorRegistry
  • box display for "axes" representation

Changed

  • ResidueindexColorMaker colorscale domain on a per chain basis
  • ChainindexColorMaker colorscale domain on a per model basis
  • Fixed, initial parameters for a Buffer not taken into account
  • ignore bonds that are defined multiple times in PDB parser
  • updated mmtf lib to v1.0
  • use npm as the build system
  • complete list of ion and saccharide group names

Removed

  • gulp as the build system

v0.8

22 Jul 21:38
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Added

  • gulp build scripts
  • mmtf v0.2 support
  • support for rendering double/triple bonds, enable via multipleBond Representation parameter (@fredludlow, @arose)
  • stage.clicked signal (renamed from .onPicking)
  • stage.hovered signal
  • parsing of "chem comp" cif files
  • experimental "axes" representation showing the principal axes of an atom selection
  • added cone, arrow & ellipsoid buffers
  • added Shape class as a simple way to add custom shapes to the scene

Changed

  • reorganized everything to use es6 modules
  • read bondOrder from 'pdbx_value_order' in mmcif files
  • interpret 'CONECT 1529 1528 1528' as double bond in pdb files
  • side Buffer/Representation parameter changed: THREE.FrontSide => "front", THREE.BackSide => "back", THREE.DoubleSide => "double"
  • support for negative resno values in selections: "-5:A", "-12--8", "-12-0"
  • use chemical component type (available in mmtf) for determining molecule type
  • .get/setOrientation return/argument changed
  • enable SDF font as the default TextBuffer class only on Chrome
  • support for building using three-jsnext
  • renamed radiusSegments parameter to radialSegments
  • WebWorkers (for building surfaces) no longer need to load the main script file
  • NGL.GET renamed to NGL.getQuery

Removed

  • python-based build scripts
  • closure-compiler
  • stage.signals.onPicking (renamed to .clicked)
  • stage.signals.atom/bond/volume/nothingPicked, use .clicked instead
  • NGL.mainScriptFilePath no longer needed
  • NGL.useWorker, use "useWorker" representation parameter

v0.7.1a

03 Jun 01:36
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Changed

  • fixed version in builds

v0.7.1

03 Jun 00:25
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Added

  • orthographic camera mode
  • backgroundColor parameter for Stage
  • x/y/z offset parameters for labels (TextBuffer)
  • OX1 atoms are recognized as part of the protein backbone
  • stage.makeImage now increments the task counter
  • added .isIdentity method to test if an Assembly is an identity transformation over all chains
  • embedded-dev build target (@sbliven)
  • support for responseType = "json" to efficiently load json data

Changed

  • there is no longer a fake unitcell created when no space group information is available
  • the query string is removed from urls before the determining file info (e.g. name, extension)
  • fixed labelText param not working in LabelRepresentation
  • enable SDF font as the default only on Chrome (fixes labels not shown on some OS/Browser)
  • ignore 'given' ncs operators
  • ensure that resname is upper case

Removed

  • stage.setTheme removed (use new backgroundColor parameter), themes now part of GUI code
  • NGL.Preferences is now part of the GUI code and removed from NGL.Stage. Setting overwritePreferences: true when instantiating an NGL.Stage object is not necessary anymore.
  • removed .requestVisibility method and signal (too GUI specific, if needed, should be handled there)

v0.7

09 May 00:02
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Added

  • Store and Proxy classes for memory efficiency
  • MMTF, DXBIN, DCD files format parsers
  • 'unitcell' representation
  • stage.makeImage (returns Promise)
  • take NCS operations into account when creating unitcell & supercell assemblies
  • added multi sample antialias rendering
  • added support for spinning around an axis
  • use bitsets for storing selections of atoms
  • Assembly and AssemblyPart classes
  • stage.toggleFullscreen method
  • read occupancy data when available (mmCIF, pdb, mmtf)
  • occupancy color scheme
  • alternate location support in selections, e.g. %B
  • read insertion codes when available (mmCIF, pdb, mmtf)
  • insertion code support in selections, e.g. ^A
  • numeric residue name support in selections, e.g. [032]
  • Queue class to handle async tasks

Changed

  • fixed transformation matrix in mrc/ccp4 parser
  • optimized near clipping
  • Fiber class remanamed to Polymer
  • more consistent fog
  • use workers more sparsely due to the large overhead of creating them
  • create font SDF on demand, remove asset dependency
  • integrated three.js lighting into custom shaders
  • MIGRATION: chainname read from auth_asym_id instead of from label_asym_id field
  • DOC: clarified apache configuration for deployment
  • FIX: cif parser, ignore non-displayable bonds between symmetry mates
  • FIX: cif parser, struct_conn bonds not added for multiple altloc atoms
  • LIB: updated signals.js
  • LIB: updated promise.js
  • LIB: updated three.js
  • LIB: updated pako.js to pako_inflate.js (no deflation support needed)
  • CODE: support loading of Blob objects in addition to File objects
  • CODE: tweaked DistanceRepresentation visibility params

Removed

  • zip, lzma, bzip2 decompression
  • removed async.js
  • mdsrv related code and documentation
  • stage.exportImage (makes image and triggers download), use stage.makeImage

v0.6

12 Oct 14:19
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release 0.6

v0.5

12 Oct 14:15
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BUILD: updated